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### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:SEMPLR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SEMPLR_1.1.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/SEMPLR.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SEMPLR/DESCRIPTION’ ... OK
* this is package ‘SEMPLR’ version ‘1.1.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SEMPLR’ can be installed ... OK
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
plotEnrich     7.373  0.219   7.681
enrichmentSets 6.561  0.215   6.876
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.24-bioc/meat/SEMPLR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL SEMPLR
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘SEMPLR’ ...
** this is package ‘SEMPLR’ version ‘1.1.0’
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c scoreSequence.cpp -o scoreSequence.o
scoreSequence.cpp: In function ‘Rcpp::DataFrame scoreSequence(Rcpp::NumericMatrix, Rcpp::CharacterVector, int, float, Rcpp::CharacterVector)’:
scoreSequence.cpp:98:50: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   98 |     if (dna_sequence.length() - last_frame_index < sem.nrow()) {
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o SEMPLR.so RcppExports.o scoreSequence.o -L/home/biocbuild/R/R-4.5.0/lib -lR
installing to /home/biocbuild/R/R-4.5.0/site-library/00LOCK-SEMPLR/00new/SEMPLR/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SEMPLR)

R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(SEMPLR)
> 
> test_check("SEMPLR")
Building background set (this may take several minutes) ...

Mapping foreground ids to ENTREZIDs...
'select()' returned 1:1 mapping between keys and columns
Successfully mapped 100% of the provided foreground ids.
Mapping background ids to ENTREZIDs...
'select()' returned 1:1 mapping between keys and columns
Successfully mapped 100% of the provided foreground ids.
Checking for inflation...
'select()' returned 1:1 mapping between keys and columns
Combining overlapping promoter ranges within genes. (This step may take 1-2 minutes)...
Defining background elements...
Building background set (this may take several minutes) ...
Scale for y is already present.
Adding another scale for y, which will replace the existing scale.
Scale for fill is already present.
Adding another scale for fill, which will replace the existing scale.
motif ignored because SNPEffectMatrix object given. See motif argument description in ?plotSEM.
Mapping foreground ids to ENTREZIDs...
'select()' returned 1:1 mapping between keys and columns
Successfully mapped 100% of the provided foreground ids.
Building background id set...
'select()' returned 1:many mapping between keys and columns
Checking for inflation...
'select()' returned 1:1 mapping between keys and columns
Mapping foreground ids to ENTREZIDs...
'select()' returned 1:1 mapping between keys and columns
Successfully mapped 100% of the provided foreground ids.
Building background id set...
'select()' returned 1:many mapping between keys and columns
Checking for inflation...
'select()' returned 1:1 mapping between keys and columns
Mapping foreground ids to ENTREZIDs...
'select()' returned 1:1 mapping between keys and columns
Successfully mapped 100% of the provided foreground ids.
Mapping background ids to ENTREZIDs...
'select()' returned 1:1 mapping between keys and columns
Successfully mapped 100% of the provided foreground ids.
Checking for inflation...
'select()' returned 1:1 mapping between keys and columns
Combining overlapping promoter ranges within genes. (This step may take 1-2 minutes)...
Defining background elements...
Mapping foreground ids to ENTREZIDs...
'select()' returned 1:1 mapping between keys and columns
Successfully mapped 100% of the provided foreground ids.
Mapping background ids to ENTREZIDs...
'select()' returned 1:1 mapping between keys and columns
Successfully mapped 100% of the provided foreground ids.
Checking for inflation...
'select()' returned 1:1 mapping between keys and columns
Combining overlapping promoter ranges within genes. (This step may take 1-2 minutes)...
Defining background elements...
Mapping foreground ids to ENTREZIDs...
'select()' returned 1:1 mapping between keys and columns
Successfully mapped 100% of the provided foreground ids.
Building background id set...
'select()' returned 1:many mapping between keys and columns
Checking for inflation...
'select()' returned 1:1 mapping between keys and columns
Mapping foreground ids to ENTREZIDs...
Mapping foreground ids to ENTREZIDs...
'select()' returned 1:1 mapping between keys and columns
Successfully mapped 100% of the provided foreground ids.
'select()' returned 1:1 mapping between keys and columns
Successfully mapped 100% of the provided foreground ids.
Checking for inflation...
'select()' returned 1:1 mapping between keys and columns
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 223 ]
> 
> proc.time()
   user  system elapsed 
 70.243   2.810  74.284